Hello Kerry,
I've committed a fix for this in 11800:a53f2f700699 to the galaxy-central branch. Is that the branch you're pulling?
Thanks for reporting this.
Greg Von Kuster
On Dec 18, 2013, at 5:48 PM, Kerry Deutsch Kerry.Deutsch@systemsbiology.org wrote:
Hello -
I pulled down the latest changes today (it was long overdue), and am running into the following error when I run the tool migration:
sh ./scripts/migrate_tools/0008_tools.sh install_dependencies No handlers could be found for logger "galaxy.tools.data" Repositories will be installed into configured tool_path location ../shed_tools [localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdWuQjBx
Skipping installation of tool dependency samtools version 0.1.18 since it is installed in /users/galaxy/galaxy_deps/bin/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d
Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module> app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py", line 83, in __init__ install_dependencies=install_dependencies ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 121, in __init__ is_repository_dependency=is_repository_dependency ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 509, in install_repository is_repository_dependency=is_repository_dependency ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 351, in handle_repository_contents guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 259, in get_guid full_path = str( os.path.abspath( os.path.join( root, name ) ) ) UnboundLocalError: local variable 'name' referenced before assignment
Ideas?
Thanks much! Kerry ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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